Sorry to disturb you！ I would like to consult the following questions:
Q1: The Maximum Likelihood（ML) tree created by iQtree contains bootstrap values in Newick tree file. Does I need to remove these values before running EasyCodeML?
Q2: When using EasyCodeML for positive selection analysis, should I exclude the outgroup in the ML construction?
Sorry to disturb you！ I would like to consult the following questions:
Q1: The Maximum Likelihood（ML) tree created by iQtree contains bootstrap values in Newick tree file. Does I need to remove these values before running EasyCodeML?
Q2: When using EasyCodeML for positive selection analysis, should I exclude the outgroup in the ML construction?